Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold756

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 32737
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:2527 original size:46 final size:46

Alignment explanation


    Indices: 2460--2588  Score: 195
    Period size: 46  Copynumber: 2.8  Consensus size: 46

       2450 TGTAACCCGC

                   *      *                *    * *       
       2460 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT

                                        *            *    
       2506 CCATAAGTGAACTCGGACTCAACTCAACCAGTTCGGACATTTGCAT
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT

                                                 
       2552 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA

       2589 TGCTCAACCA


Statistics
Matches: 75,  Mismatches: 8, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  46   75  1.00

ACGTcount: A:0.30, C:0.29, G:0.20, T:0.20


Consensus pattern (46 bp):   
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT

Found at i:2607 original size:46 final size:45

Alignment explanation


    Indices: 2468--2607  Score: 122
    Period size: 46  Copynumber: 3.0  Consensus size: 45

       2458 GCCCATAAGC

                  *                *    **     *           
       2468 GAACTCAGACTCAACTCAACGAGCTCGGGCGTTC-GCATCCATAAGT
          1 GAACTCGGACTCAACTCAACGAGTTCGGATGTTCACCATCC-T-AGT

                                *        **   **           
       2514 GAACTCGGACTCAACTCAACCAGTTCGGACATT-TGCATCCATAAGT
          1 GAACTCGGACTCAACTCAACGAGTTCGGATGTTCACCATCC-T-AGT

                                           *              
       2560 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAGT
          1 GAACTCGGACTCAACTCAACGAGTTCGGATGTTC-ACCATCCTAGT

              
       2606 GA
          1 GA

       2608 CATGTCACTT


Statistics
Matches: 80,  Mismatches: 11, Indels: 6
        0.82            0.11        0.06

Matches are distributed among these distances:
  46   74  0.93
  47    1  0.01
  48    5  0.06

ACGTcount: A:0.29, C:0.29, G:0.20, T:0.21


Consensus pattern (45 bp):   
GAACTCGGACTCAACTCAACGAGTTCGGATGTTCACCATCCTAGT

Found at i:5947 original size:13 final size:13

Alignment explanation


    Indices: 5929--5953  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       5919 CCGTGCCCTT

                         
       5929 CACATGGCTGTGA
          1 CACATGGCTGTGA

                        
       5942 CACATGGCTGTG
          1 CACATGGCTGTG

       5954 TCTCTGCCCC


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.20, C:0.24, G:0.32, T:0.24


Consensus pattern (13 bp):   
CACATGGCTGTGA

Found at i:18864 original size:16 final size:16

Alignment explanation


    Indices: 18840--18874  Score: 61
    Period size: 16  Copynumber: 2.2  Consensus size: 16

      18830 TCGCGATAAC

                            
      18840 AGTTAGTTTATGAACG
          1 AGTTAGTTTATGAACG

                *           
      18856 AGTTTGTTTATGAACG
          1 AGTTAGTTTATGAACG

               
      18872 AGT
          1 AGT

      18875 AATTATAAAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  16   18  1.00

ACGTcount: A:0.29, C:0.06, G:0.26, T:0.40


Consensus pattern (16 bp):   
AGTTAGTTTATGAACG

Found at i:29304 original size:20 final size:22

Alignment explanation


    Indices: 29264--29304  Score: 59
    Period size: 20  Copynumber: 2.0  Consensus size: 22

      29254 GCCAAACCCT

                            *     
      29264 CTGATTCTTCTCCATCTTTTGG
          1 CTGATTCTTCTCCATCCTTTGG

                                 
      29286 CTGATTC-TCT-CATCCTTTG
          1 CTGATTCTTCTCCATCCTTTG

      29305 AACCCCAAAG


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  20    8  0.44
  21    3  0.17
  22    7  0.39

ACGTcount: A:0.10, C:0.29, G:0.12, T:0.49


Consensus pattern (22 bp):   
CTGATTCTTCTCCATCCTTTGG

Found at i:30950 original size:39 final size:39

Alignment explanation


    Indices: 30875--31018  Score: 200
    Period size: 39  Copynumber: 3.7  Consensus size: 39

      30865 ACCAGCTCGA

                           *  *     *   *   *     * 
      30875 AGCCTGCGAGA-CTTTAGCCCGGACATATTTCTAGCACGT
          1 AGCCTGCG-GACCTTAAGTCCGGATATAATTCCAGCACAT

                                  * *              
      30914 AGCCTGCGGACCTTAAGTCCGGTTTTAATTCCAGCACAT
          1 AGCCTGCGGACCTTAAGTCCGGATATAATTCCAGCACAT

                                                   
      30953 AGCCTGCGGACCTTAAGTCCGGATATAATTCCAGCACAT
          1 AGCCTGCGGACCTTAAGTCCGGATATAATTCCAGCACAT

                                       
      30992 AGCCTGCGGACCTTAAGTCCGGATATA
          1 AGCCTGCGGACCTTAAGTCCGGATATA

      31019 CTTCATCACT


Statistics
Matches: 94,  Mismatches: 10, Indels: 2
        0.89            0.09        0.02

Matches are distributed among these distances:
  38    2  0.02
  39   92  0.98

ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25


Consensus pattern (39 bp):   
AGCCTGCGGACCTTAAGTCCGGATATAATTCCAGCACAT
Done.